Supplemental Material for Huang et al., 2018
datasetposted on 2018-10-01, 13:06 authored by Zhongyun Huang, Shannon Kelly, Rika Matsuo, Lin-Feng Li, Yaling Li, Kenneth M. Olsen, Yulin Jia, Ana L. Caicedo
Supplementary tables contain genotype and phenotype of Oryza accessions included in the study, and genomic regions sequenced by target capture. Figure S1 contains phylogeny tree based on SNPs.
A series of in-house Perl scripts to convert the polymorphisms from variant call format (VCF) to FASTA format; estimate of nucleotide diversity including Nei’s average pairwise nucleotide diversity (π) and Watterson’s estimator of theta (θw)
Fasta format files of gene fragments (~1500 base pair) upstream and downstream of the five candidate genes. These fragments were captured following the Agilent (Agilent, Santa Clara, CA) SureSelect Target Enrichment method (Gnirke et al., 2009). A total of 123 loci close to the five candidate genes were targeted and sequenced (Table S2)